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Bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae is a major biotic constraint on obtaining higher grain yields in rice. Marker-assisted backcross breeding (MABB) was performed by the pyramiding of Xa4, xa5, xa13 and Xa21 resistance genes in the popular variety, Ranidhan. A foreground selection in BC1F1, BC2F1, and BC3F1 progenies detected all the target genes in 12, 7 and 16 progenies by using the closely linked markers from a population size of 426, 410, and 530, respectively. The BB-positive progenies carrying the target genes with a maximal similarity to the recipient parent was backcrossed in each backcross generation. A total of 1784 BC3F2 seeds were obtained from the best BC3F1 progeny. The screening of the BC3F2 progenies for the four target genes resulted in eight plants carrying all the four target genes. A bioassay of the pyramided lines conferred very high levels of resistance to the predominant isolates of bacterial blight disease. In addition, these pyramided lines were similar to Ranidhan in 16 morpho-quality traits, namely, plant height, filled grains/panicle, panicles/plant, grain length, grain breadth, grain weight, milling, head rice recovery, kernel length after cooking, water uptake, the volume expansion ratio, gel consistency, alkali-spreading value, and the amylose content.

The underground reserve (root) has been an uncharted research territory with its untapped genetic variation yet to be exploited. Identifying ideal traits and breeding new rice varieties with efficient root system architecture (RSA) has great potential to increase resource-use efficiency and grain yield, especially under direct-seeded rice, by adapting to aerobic soil conditions. In this review, we tried to mine the available research information on the direct-seeded rice (DSR) root system to highlight the requirements of different root traits such as root architecture, length, number, density, thickness, diameter, and angle that play a pivotal role in determining the uptake of nutrients and moisture at different stages of plant growth. RSA also faces several stresses, due to excess or deficiency of moisture and nutrients, low or high temperature, or saline conditions. To counteract these hindrances, adaptation in response to stress becomes essential. Candidate genes such as early root growth enhancer PSTOL1, surface rooting QTL qSOR1, deep rooting gene DRO1, and numerous transporters for their respective nutrients and stress-responsive factors have been identified and validated under different circumstances. Identifying the desired QTLs and transporters underlying these traits and then designing an ideal root architecture can help in developing a suitable DSR cultivar and aid in further advancement in this direction.

Flash flooding (FF) along with bacterial blight (BB) outbreak are very destructive for rice production in the rainfed shallow-lowland (RSL) ecosystem. The presence of dynamic Xoo races with varying levels of genetic diversity and virulence renders their management extremely challenging under RSL. In this context, the marker-assisted improvement of plant resistance/tolerance has been proven as one of the most promising strategies towards the development of sustainable cultivars. The present study demonstrates the marker-assisted introgression of the submergence tolerant (Sub1) and three bacterial blight resistant genes (Xa21 + xa13 + xa5) into the genetic background of Hasanta, a long duration popular rice variety in the eastern coastal region of India. The rice genotypes, Swarna Sub1 (carrying Sub1) and IRBB66 (carrying Xa21 + xa13 + Xa7 + xa5 + Xa4) had maximum genetic similarity (0.84 and 0.73, respectively) with Hasanta; recurrent parent (RP) was used as donor. The forward analysis of target genes in F1s, IC1F1s and backcross (BC) generations was performed by linked/genic markers (Sub1bc2; pTA248, xa13prom and RM122), whereas background recovery of RP in each BC and segregating generations was performed utilizing 108 hypervariable SSR markers. Intervened speed breeding (SB) strategy and intensive phenotyping could lead the development of near isogenic lines (NILs) as to the RP in all basic traits. The performance of the near isogenic lines (NILs, BC2F3 and BC2F4), HS 232-411-391-756-37, HS 232-411-391-809-8, HS 232-411-391-756-18, HS 110-224-197-10-36, HS 232-411-391-809-81, HS 110-224-197-10-41 and HS 232-411-391-809-63 establishes the utility of marker-assisted backcross-breeding (MAB) and SB in accelerated trait introgression. The introgressed lines carrying Sub1 + Xa21 + xa13 + xa5 showed 76% to 91% survival under 14 days of submergence and durable BB resistance (percent disease index-PDI of 2.68 ± 0.26 to 6.22 ± 1.08 and lesion length, LL of 1.29 ± 0.12 to 4.2 ± 0.64 cm). Physiological analysis revealed that improved NILs, carrying Sub1 gene conquered adaptive physiological modulations, had reduced the consumption of soluble sugar and the degradation of total chlorophyll contents (TCC), and an enhanced level of Alcohol Dehydrogenase activity (ADH) and proline accumulation in all submergence regimes. The pyramided lines attained complete product profile of RP, that will contribute to sustainable rice production under RSL, particularly in the coastal region that has substantial acreage under the variety Hasanta.

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Twenty eight inter simple sequence repeat (ISSR) markers were used to determine the genotypic identification and phylogenetic relationship within 48 varieties of Indica rice including four aromatic rice grown in eastern part of India. Out of 44 upland and low land varieties, 39 varieties released by the Orissa University of Agriculture and Technology, Orissa and five released by the other National Institutes of India. A total of 28 ISSR primers were screened representing di-and tri-nucleotide repeats, out of which 12 ISSR markers were selected for varietal analysis as diagnostic markers. The number of bands per locus ranged from 4 to 8, with an average of 6. The results revealed that all the primers showed distinct polymorphism among the varieties indicating the robust nature of ISSR markers. Most of the primers showed highest polymorphic information content and resolving power. The cluster analysis indicates that all the rice genotypes are grouped into two classes in which aromatic rice varieties clustered separately from upland and lowland varieties. Principal component analysis showed the distinct differences among themselves. Based on this study, the larger range of similarity values using ISSR markers provides greater confidence for the assessment of genetic relationships among the varieties. The information obtained from the DNA profile helps to identify the variety diagnostic markers in 48 rice genotypes. This outcome of the investigation can be used in background selections during backcross breeding programs.

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The microsatellite or simple sequence repeat (SSR) markers were used to determine the allelic diversity and relationship among 48 traditional indigenous aromatic rice germplasm grown under Eastern part of India. Out of 30 primers, 12 primers showed DNA amplification and polymorphism among 48 aromatic rice genotypes. A total of 28 bands appeared by using 12 SSR primers in 48 aromatic rice varieties/landraces. The number of alleles per locus ranged from 1 to 5 with an average 2.08. Out of 28 bands, 25 bands were polymorphic and three were monomorphic bands. The results reveal that all the tested primers showed distinct polymorphism among the landraces/varieties indicating the robust nature of SSR markers. Most of the primers showed highest polymorphic information content (PIC). Phenotypic characteristics are significantly correlated with genotypic characters. The cluster analysis indicates that the 48 traditional indigenous aromatic rice genotypes were grouped into two major clusters. Among the two major clusters, one cluster had 11 varieties and the second cluster had 37 varieties on the basis of the group of land races. Based on this study, the larger range of similarity values using SSR markers provides greater confidence for the assessment of genetic relationships among the varieties. The information obtained from the SSR profile helps to identify the variety diagnostic markers in 48 traditional indigenous aromatic rice genotypes. Significant genetic variation at maximum number of loci between varieties indicates rich genetic resources in rice. The intra and inter genetically variation might be useful for breeders to improve the aromatic rice varieties through selective breeding and cross breeding programs and also protect these unique germplasm under Intellectual Property Rights (IPR).